Method for treating a semiconductor device

ABSTRACT

A method of treating a sensor array including a plurality of sensors and an isolation structure, where a sensor of the plurality of sensors has a sensor pad exposed at a surface of the sensor array and the isolation structure is disposed between the sensor pad and sensor pads of other sensors of the plurality of sensors, comprises exposing the sensor pad and the isolation structure to a non-aqueous organo-silicon solution including an organo-silicon compound and a first non-aqueous carrier; applying an acid solution including an organic acid and a second non-aqueous carrier to the sensor pad; and rinsing the acid solution from the sensor pad and the isolation structure.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application is a continuation application under 35 U.S.C. § 120 ofpending U.S. application Ser. No. 16/182,429 filed Nov. 6, 2018 (soonU.S. Pat. No. 10,456,814), which is a continuation of U.S. applicationSer. No. 15/387,591 filed Dec. 21, 2016 (now U.S. Pat. No. 10,137,480),which is a divisional of U.S. application Ser. No. 15/079,532 filed Mar.24, 2016 (now U.S. Pat. No. 9,555,451), which claims benefit under 35U.S.C. § 119(e) of U.S. Provisional Application No. 62/138,537 filedMar. 26, 2015. The entire contents of the aforementioned applicationsare incorporated by reference herein.

NOTICE OF INCLUSION OF A COPYRIGHT OR MASK WORK NOTICE

A portion of the disclosure of this patent document contains materialwhich is subject to (copyright or mask work) protection. The (copyrightor mask work) owner has no objection to the facsimile reproduction byanyone of the patent document or the patent disclosure, as it appears inthe Patent and Trademark Office patent file or records, but otherwisereserves all (copyright or mask work) rights whatsoever.

FIELD OF THE DISCLOSURE

This disclosure, in general, relates to methods for treating sensorarrays, sensor arrays formed by such methods, and solutions for use insuch methods.

BACKGROUND

Arrays of sensors formed in semiconductor substrates are increasinglybeing used in fields such as analytical chemistry and molecular biology.For example, when analytes are captured on or near sensor pads of asensor array, the analytes or byproducts of reactions associated withthe analytes can be detected and used to elucidate information regardingthe analyte. In particular, such sensor arrays have found use in geneticanalysis, such as genetic sequencing or quantitative amplification.

During manufacture, various semiconductor processing techniques canalter the nature of the surface of a sensor array and the surface ofwell structures around the sensor array. Such processing can also leaveresidues on the surface. Altered surface chemistry or residues canprevent or limit the capture of analytes proximate to the sensors. Assuch, the effectiveness of such sensor arrays is reduced, and signalsresulting from such sensor arrays may include erroneous data or no data.

SUMMARY

In an aspect, a sensor device including a sensor array and optionally anisolation structure, such as a well array, corresponding to the sensorarray or a lid attached over the sensor array can be treated with atreatment solution. The treatment solution can include an organicsolvent, an organic acid, and an organo-silicon compound. Alternatively,the sensor array can be exposed to an organo-silicon solution includingthe organo-silicon compound and a non-aqueous carrier, followed byapplication of an acid solution including the organic acid and anon-aqueous carrier. The sensor device can be further treated with abasic solution, such as a NaOH solution, or can be rinsed with a lowboiling organic solvent or water. Optionally, the sensor device can bedried.

BRIEF DESCRIPTION OF THE DRAWINGS

The present disclosure may be better understood, and its numerousfeatures and advantages made apparent to those skilled in the art byreferencing the accompanying drawings.

FIG. 1 includes an illustration of an exemplary measurement system.

FIG. 2 includes an illustration of an exemplary measurement component.

FIG. 3 includes an illustration of exemplary array of measurementcomponents.

FIG. 4 includes an illustration of exemplary well configurations.

FIG. 5 includes an illustration of exemplary well and sensorconfigurations.

FIG. 6 and FIG. 7 include illustrations of exemplary sensor devices.

FIG. 8, FIG. 9, FIG. 10, and FIG. 11 include flow diagrams illustratingexemplary methods.

FIG. 12 includes an illustration of exemplary methods for preparing asequencing device.

FIG. 13, FIG. 14, FIG. 15, and FIG. 16 include graphs illustrating theinfluence of organo-silicon compounds on sequencing performance.

The use of the same reference symbols in different drawings indicatessimilar or identical items.

DETAILED DESCRIPTION

In an exemplary embodiment, a method for treating a sensor arrayincludes applying a treatment solution to the sensor array and rinsingthe treatment solution from the sensor array. In particular, thetreatment solution can include an organic solvent, an organic acid, andan organo-silicon compound. Alternatively, the sensor array can beexposed to an organo-silicon solution including the organo-siliconcompound and a non-aqueous carrier, followed by application of an acidsolution including the organic acid and a non-aqueous carrier. Theorgano-silicon compound can be a silane, siloxane, or silazane compound,derivative thereof, or any combination thereof. The organo-siliconcompound can include a termination moiety, such as an alkyl, vinyl, orhydride moiety, or any combination thereof. The acid can be a sulfonicacid, such as an alkyl or alkyl aryl sulfonic acid. In an example, thealkyl or alkyl aryl sulfonic acid can have an alkyl group having between9 and 18 carbons. For example, the sulfonic acid can include dodecylbenzene sulfonic acid (DBSA). The organic solvent or the non-aqueouscarrier can be a non-polar solvent or an aprotic polar solvent. In anexample, the organic solvent can have a normal boiling point a range of65° C. to 275° C. In an example, the organic solvent includes heptane.In another example, the organic solvent includes undecane.

Following treatment with the treatment solution, the sensor array can berinsed with a rinse solution. In an example, the rinse solution includesa low boiling organic solvent such as alcohol, for example, ethanol orisopropanol. In another example, the rinse solution can include water.The method can further include applying a basic solution or a weak acidsolution following application of the treatment solution and beforerinsing. The basic solution can have a pH of greater than 7, such as atleast 8, but generally not greater than 14, and can include a strongbase, such as sodium hydroxide. In an example, the treatment solutionand the basic solution can be applied repeatedly, such as 2 or moretimes, 3 or more times or even 4 or more times, but generally notgreater than 10 times.

In a particular embodiment, a treatment solution is applied to at leasta sensor pad of the sensor array. The sensor array can include aplurality of sensors. A sensor of the sensor array can include a sensorpad. Optionally, a well structure can be defined over the sensor arrayand include a plurality of wells correspond with sensor pads of thesensor array. A well of the well array can expose a sensor pad of asensor. Optionally, a lid including at least one fluid port can bedisposed or attached over the sensor array and the well structure. Aspace for fluid can be defined between the lid and the well structure orsensor array and can be in fluid communication with the fluid port ofthe lid. The treatment solution can be applied through the fluid portand into the space between the lid and the well structure. Optionally, abasic solution can be applied through the fluid port to the spacebetween the lid and the well structure following application of thetreatment solution. Application of the treatment solution followed bythe basic solution can be repeated, such as at least twice or even atleast 3 times, but generally not greater than 10 times. A rinse solutioncan be applied through the fluid port, for example, including alcohol orwater. Optionally, the system can be dried.

In another exemplary embodiment, a sensor array includes a plurality ofsensors. A sensor of the plurality of sensors includes a sensor pad. Awell structure is disposed over the sensor array and includes a wellarray that operatively corresponds with the sensor array. A well of thewell array exposes a sensor pad of a sensor. The treatment solutionincluding an organo-silicon compound, an acid, such as a sulfonic acid,and an organic solvent can be applied to the sensor array for a periodbetween 30 seconds and 30 minutes. The sensor array can be rinsed with arinse solution. In an example, the rinse solution can include a lowboiling organic solvent, such as an alcohol. The sensor array can berinsed one or more times with the low boiling organic solvent. Inanother example or in addition, the sensor array can be rinsed withwater, such as deionized water. The sensor array can be dried and a lidcan be attached over the well structure and the sensor array. The lidcan include at least one fluid port. A space is defined between the lidand the sensor array or the well structure and is in fluid communicationwith the fluid port.

In a particular embodiment, a sensor system includes a flow cell inwhich a sensory array is disposed, includes communication circuitry inelectronic communication with the sensory array, and includes containersand fluid controls in fluidic communication with the flow cell. In anexample, FIG. 1 illustrates an expanded and cross-sectional view of aflow cell 100 and illustrates a portion of a flow chamber 106. A reagentflow 108 flows across a surface of a well array 102, in which thereagent flow 108 flows over the open ends of wells of the well array102. The well array 102 and a sensor array 105 together can form anintegrated unit forming a lower wall (or floor) of flow cell 100. Areference electrode 104 can be fluidly coupled to flow chamber 106.Further, a flow cell cover 130 encapsulates flow chamber 106 to containreagent flow 108 within a confined region.

FIG. 2 illustrates an expanded view of a well 201 and a sensor 214, asillustrated at 110 of FIG. 1. The volume, shape, aspect ratio (such asbase width-to-well depth ratio), and other dimensional characteristicsof the wells can be selected based on the nature of the reaction takingplace, as well as the reagents, byproducts, or labeling techniques (ifany) that are employed. The sensor 214 can be a chemical field-effecttransistor (chemFET), more specifically an ion-sensitive FET (ISFET),with a floating gate 218 having a sensor plate 220 optionally separatedfrom the well interior by a material layer 216. In addition, aconductive layer (not illustrated) can be disposed over the sensor plate220. In an example, the material layer 216 includes an ion sensitivematerial layer. The material layer 216 can be a ceramic layer, such asan oxide of zirconium, hafnium, tantalum, aluminum, or titanium, amongothers, or a nitride of titanium. In an example, the material layer 216can have a thickness in a range of 5 nm to 100 nm, such as a range of 10nm to 70 nm, a range of 15 nm to 65 nm, or even a range of 20 nm to 50nm. Together, the sensor plate 220 and the material layer 216 form asensor pad.

While the material layer 216 is illustrated as extending beyond thebounds of the illustrated FET component, the material layer 216 canextend along the bottom of the well 201 and optionally along the wallsof the well 201. The sensor 214 can be responsive to (and generate anoutput signal related to) the amount of a charge 224 present on materiallayer 216 opposite the sensor plate 220. Changes in the charge 224 cancause changes in a current between a source 221 and a drain 222 of thechemFET. In turn, the chemFET can be used directly to provide acurrent-based output signal or indirectly with additional circuitry toprovide a voltage-based output signal. Reactants, treatment solutions,and other reagents can move in and out of the wells by a diffusionmechanism 240.

In an embodiment, reactions carried out in the well 201 can beanalytical reactions to identify or determine characteristics orproperties of an analyte of interest. Such reactions can generatedirectly or indirectly byproducts that affect the amount of chargeadjacent to the sensor plate 220. If such byproducts are produced insmall amounts or rapidly decay or react with other constituents,multiple copies of the same analyte can be analyzed in the well 201 atthe same time in order to increase the output signal generated. In anembodiment, multiple copies of an analyte can be attached to a solidphase support 212, either before or after deposition into the well 201.In an example, the solid phase support 212 can be a particle, such as apolymeric particle or an inorganic particle. In another example, thesolid phase support 212 can be a polymer matrix, such as a hydrophilicpolymer matrix, for example, a hydrogel matrix or the like.

The well 201 can be defined by a wall structure, which can be formed ofone or more layers of material. In an example, the wall structure canhave a thickness extending from the lower surface to the upper surfaceof the well in a range of 0.01 micrometers to 10 micrometers, such as arange of 0.05 micrometers to 10 micrometers, a range of 0.1 micrometersto 10 micrometers, a range of 0.3 micrometers to 10 micrometers, or arange of 0.5 micrometers to 6 micrometers. In particular, the thicknesscan be in a range of 0.01 micrometers to 1 micrometer, such as a rangeof 0.05 micrometers to 0.5 micrometers, or a range of 0.05 micrometersto 0.3 micrometers. The wells 201 can have a characteristic diameter,defined as the square root of 4 times the cross-sectional area (A)divided by Pi (e.g., sqrt(4*A/π), of not greater than 5 micrometers,such as not greater than 3.5 micrometers, not greater than 2.0micrometers, not greater than 1.6 micrometers, not greater than 1.0micrometers, not greater than 0.8 micrometers or even not greater than0.6 micrometers. In an example, the wells 201 can have a characteristicdiameter of at least 0.01 micrometers.

While FIG. 2 illustrates a single-layer wall structure and asingle-layer material layer 216, the system can include one or more wallstructure layers, one or more conductive layers or one or more materiallayers. For example, the wall structure can be formed of one or morelayers, including an oxide of silicon or TEOS or including a nitride ofsilicon.

In a particular example illustrated in FIG. 3, a system 300 includes awell wall structure 302 defining an array of wells 304 disposed over oroperatively coupled to sensor pads of a sensor array. The well wallstructure 302 defines an upper surface 306. A lower surface 308associated with the well is disposed over a sensor pad of the sensorarray. The well wall structure 302 defines a sidewall 310 between theupper surface 306 and the lower surface 308. As described above, amaterial layer in contact with sensor pads of the sensor array canextend along the lower surface 308 of a well of the array of wells 304or along at least a portion of the wall 310 defined by the well wallstructure 302. The upper surface 306 can be free of the material layer.In some examples, at least a portion of the well wall structure 302 isnot covered by the material layer.

While the wall surface of FIG. 2 is illustrated as extendingsubstantially vertically and outwardly, the wall surface can extend invarious directions and have various shapes. Substantially verticallydenotes extending in a direction having a component that is normal tothe surface defined by the sensor pad. For example, as illustrated inFIG. 4, a well wall 402 can extend vertically, being parallel to anormal component 412 of a surface defined by a sensor pad. In anotherexample, the wall surface 404 extends substantially vertically, in anoutward direction away from the sensor pad, providing a larger openingto the well than the area of the lower surface of the well. Asillustrated in FIG. 4, the wall surface 404 extends in a directionhaving a vertical component parallel to the normal component 412 of thesurface 414. In an alternative example, a wall surface 406 extendssubstantially vertically in an inward direction, providing an openingarea that is smaller than an area of the lower surface of the well. Thewall surface 406 extends in a direction having a component parallel tothe normal component 412 of the surface 414.

While the surfaces 402, 404, or 406 are illustrated by straight lines,some semiconductor or CMOS manufacturing processes can result instructures having nonlinear shapes. In particular, wall surfaces, suchas wall surface 408 and upper surfaces, such as upper surface 410, canbe arcuate in shape or take various nonlinear forms. While thestructures and devices illustrated herewith are depicted as havinglinear layers, surfaces, or shapes, actual layers, surfaces, or shapesresulting from semiconductor processing can differ to some degree,possibly including nonlinear and arcuate variations of the illustratedembodiment.

FIG. 5 includes an illustration of exemplary wells including ionsensitive material layers. For example, a well structure 502 can definean array of wells, such as exemplary wells 504, 506, or 508. The wells(504, 506, or 508) can be operatively coupled to an underlying sensor(not illustrated) or linked to such an underlying sensor. Exemplary well504 includes an ion sensitive material layer 510 defining the bottom ofthe well 504 and extending into the structure 502. While not illustratedin FIG. 5, a conductive layer, such as a gate, for example, a floatinggate of ion sensitive field effect transistor can reside below the ionsensitive material layer 510.

In another example, as illustrated by well 506, an ion sensitivematerial layer 512 can define the bottom of the well 506 withoutextending into the structure 502. In a further example, a well 508 caninclude an ion sensitive layer 514 that extends along at least a portionof a sidewall 516 of the well 508 defined by the structure 502. Asabove, the ion sensitive material layers 512 or 514 can reside overconductive layers or gates of underlying electronic devices.

As illustrated in FIG. 6, the sensor device can include a sensor array602 formed within a semiconductor substrate. A well structure is definedover the sensor array. A lid 604 is attached to the well structure orthe sensor array 602. For example, the lid 604 can be adhered to thesensor array or well structure 602 using an adhesive. The lid 604includes fluid ports 606 or 608, which are in fluid communication with aflow cell 610 defined between the lid 604 and the sensor array and wellarray 602. Fluid applied to one of the fluid ports 606 or 608 can flowthrough the flow cell 610 and optionally out the other port 608 or 606.In another example illustrated in FIG. 7, a lid 702 can include fluidports 704 and 706 and can define a larger flow space. The lid can beadhered over a well array or sensor array, for example, using anadhesive.

As illustrated in the method 800 of FIG. 8, a sensor array can beexposed to a non-aqueous treatment solution including, an organo-siliconcompound and an acid, such as sulfonic acid, phosphonic acid, or acombination thereof, as illustrated 802. The treatment solution canfurther include an organic solvent.

In an example, the organo-silicon compound can include a silane, asiloxane, a silazane, a derivative thereof, or a combination thereof. Inan example, the organo-silicon compound can include a siloxane, such asa polydialkyl siloxane. In another example, the organo-silicon compoundcan include a polysilazane or a cyclic silazane. Further, theorgano-silicon compound can include a terminal moiety, such as an alkyl,vinyl, halyl, sulfonyl, hydroxyl, or hydride moiety, or any combinationthereof.

An exemplary silane includes a silane functionalized with a moiety, suchas an aryl, polyaryl, alkyl, alkoxyl, halyl, or cyano moiety, or anycombination thereof. For example, the silane can includephenyldimethylchlorosilane, tert-butylchlorodiiphenylsilane,chlorotripropylsilane, (N,N-dimethylamino) trimethyl-silane,tris(trimethylsilyl)silane, triethylchlorosilane,3-cyanopropyldimethylchloro-silane, chlorotriethylsilane,1,2-bis(chlorodimethylsiyl)ethane, trimethylsilyltrifluoronesulfonate,trioctylsilane, dodecyldimethylchlorosilane, chlorodimethylthexylsilane,trimethylchlorosilane, chloro(chloromethyl) dimethylsilane,thexyldimethylchlorosilane, triisopropylchlorosilane,trimethylmethoxysilane, trimethylchlorosilane, chlorotriisopropylsilane,acetoxytrimethylsilane, or a combination thereof.

In an example, the organo-silicon compound includes a siloxane, such asa polysiloxane, for example, including, aryl, dialkyl or alkylhydrounits, or combinations thereof. The alkyl moieties of the dialkyl oralkylhydro units can include methyl, ethyl, propyl, butyl moieties, orany combination thereof. The aryl units can include a phenylalkylsiloxyl unit, such as a phenylmethyl siloxyl unit. The polysiloxane caninclude a terminal moiety, such as an alkyl, vinyl, halyl, sulfonyl,hydroxyl, or hydride moiety, or any combination thereof. For example,the terminal moiety can include an alkyl, vinyl, hydroxyl, or hydridemoiety, or a combination thereof. In particular, the terminal moiety caninclude an alkyl, vinyl, or hydride moiety. An exemplary alkyl terminalmoiety can include a methyl, ethyl, propyl or butyl terminal moiety.

In particular, an exemplary siloxane includes an alkyl terminatedpolydimethylsiloxane (PDMS), a hydride-terminated polydimethylsiloxane(PDMS), a monovinyl terminated polydimethylsiloxane (PDMS),dichloro-tetramethyldisiloxane, hexamethyltrisiloxane,polymethylhydrosiloxane, tris(trimethylsilyloxy)silane,octamethyltrisiloxane, or a combination thereof. For example, thesiloxane can include methyl terminated polydimethylsiloxane (e.g. A,below, where “n” is between 1 and 100, such as between 2 and 50, orbetween 2 and 20), a vinyl terminated polydimethylsiloxane (e.g., B,below, wherein “n” is between 1 and 100, such as between 2 and 50, orbetween 2 and 20), a poly dimethyl methylhydro siloxane (e.g., C, below,wherein “m” is between 1 and 100, such as between 2 and 50, or between 2and 20, and “n” is between 1 and 100, such as between 2 and 50, orbetween 2 and 20), a butyl terminated polydimethylsiloxane (e.g., D,below, wherein “n” is between 1 and 100, such as between 2 and 50, orbetween 2 and 20), or a combination thereof.

In another example, a siloxane has the formula E below, wherein R caninclude a hydrophilic, polar, or amphiphilic moiety, or a combinationthereof. For example, R can include a polyalkylene oxide moiety. Inanother example, R can include pyrrolidone functionality. In a furtherexample, R can include a furan moiety. In an additional example, R caninclude a cyanoalkyl functionality. In another example, R can include anisostearyl alcohol moiety.

An exemplary silazane includes hexamethylcyclotrisilazane.

In a particular example, the organo-silicon compound has a molecularweight in a range of 50 Da to 10000 Da. For example, the molecularweight can be in a range of 100 Da to 8000 Da, such as a range of 500 Dato 7000 Da, a range of 700 Da to 6000 Da, a range of 900 Da to 6000 Da,or a range of 1200 Da to 6000 Da. In an example, the organo-siliconcompound includes a polydimethylsiloxane having a molecular weight in arange 100 Da to 8000 Da, such as a range of 500 Da to 7000 Da, a rangeof 700 Da to 6000 Da, a range of 900 Da to 6000 Da, or a range of 1200Da to 6000 Da.

The organo-silicon compound can be included in the treatment solution inan amount in a range of 0.001% to 10.0% by weight. For example, theorgano-silicon compound can be included in a range of 0.005% to 10.0%,such as a range of 0.005% to 5.0%, a range of 0.01% to 5.0%, a range of0.5% to 2.0%, or a range of 0.5% to 1.0% by weight.

The treatment solution can also include a platinum compound, such as aplatinum ligand compound. In an example, the ligand can be a vinylterminated cyclic siloxane, such as cyclic tetra (methylvinyl siloxane).In a particular example, the platinum compound has the configuration Fbelow. The treatment solution can include the platinum compound in anamount in a range of 0.0005% to 1.0% by weight, such as a range of0.005% to 0.5% or a range of 0.01% to 0.1% by weight.

An exemplary sulfonic acid includes an alkyl sulfonic acid, an alkylaryl sulfonic acid, or a combination thereof. An exemplary alkylsulfonic acid includes an alkyl group having 1 to 18 carbons, such as 1to 14 carbons, 1 to 10 carbons, or 1 to 5 carbons. In another example,the alkyl group of the alkyl sulfonic acid has 10 to 14 carbons. Forexample, an alkyl sulfonic acid can include methanesulfonic acid,ethanesulfonic acid, propane sulfonic acid, butane sulfonic acid, orcombinations thereof. In another example, the alkyl group can befunctionalized, for example, with a terminal functional group oppositethe sulfonic acid functional group. An exemplary functionalized alkylsulfonic acid includes an alkyl sulfonic acid functionalized with aterminal amine group, such as taurine. In a further example, the alkylgroups of the sulfonic acid can be halogenated, such as fluorinated.

In a further example, the sulfonic acid includes an alkyl aryl sulfonicacid. The alkyl aryl sulfonic acid, for example, alkyl benzene sulfonicacid, can include an alkyl group having between 1 and 20 carbons. Forexample, the alkyl group can have between 9 and 18 carbons, such asbetween 10 and 14 carbons. In a particular example, the alkyl arylsulfonic acid includes dodecyl benzene sulfonic acid (DBSA). The dodecylbenzene sulfonic acid (DBSA) can be a purified form of dodecyl benzenesulfonic acid having at least 90%, such as at least 95% of alkyl arylsulfonic acid having an alkyl group with 12 carbons. Alternatively, thedodecyl benzene sulfonic acid can include a blend of alkyl benzenesulfonic acid having alkyl groups with an average of 12 carbons. Thealkyl aryl sulfonic acid can be alkylated at a blend of positions alongthe alkyl chain. In another example, the alkyl group can have between 1and 6 carbons. For example, the alkyl aryl sulfonic acid can includetoluene sulfonic acid.

The treatment solution can have a concentration between 10 mM and 500 mMacid, such as sulfonic acid. For example, the treatment solution canhave a concentration between 50 mM and 250 mM acid. In another example,the treatment solution includes between 0.5 wt % and 25 wt % of theacid, such as sulfonic acid. For example, the treatment solution caninclude between 1 wt % and 10 wt % of the acid, such as between 2.5 wt %and 5 wt % of the acid, such as sulfonic acid.

The organic solvent within the treatment solution is a non-aqueoussolvent providing solubility for the acid (e.g., sulfonic acid) to atleast the concentrations above. In an example, the organic solvent canbe aprotic. The organic solvent can be a non-polar organic solvent. Inanother example, the organic solvent can be a polar aprotic solvent. Inan example, the organic solvent can have a normal boiling point in arange of 36° C. to 345° C. For example, the normal boiling point can bein a range of 65° C. to 275° C. In another example, the normal boilingpoint can be in a range of 65° C. to 150° C. Alternatively, the normalboiling point is in a range of 150° C. to 220° C.

In a particular example, the non-polar organic solvent includes analkane solvent, an aromatic solvent, or a combination thereof. An alkanesolvent can have between 6 and 20 carbons. For example, the alkane canhave between 6 and 14 carbons, such as between 6 and 9 carbons.Alternatively, the alkane can have between 10 and 14 carbons. In aparticular example, the alkane is a linear alkane. For example, thealkane solvent can include pentane, hexane, heptanes, octane, decane,undecane, dodecane, or combinations thereof. In another example, thealkane is halogenated. An exemplary branched alkane can includehydrogenated dimers of C11 or C12 alpha olefins.

In a further example, the organic solvent can include a polar aproticsolvent. For example, the polar aprotic solvent can includetetrahydrofuran, ethylacetate, acetone, dimethylformamide, acetonitrile,dimethyl sulfoxide, N-methyl pyrrolidone (NMP), or a combinationthereof. In another example, the organic solvent may be free of ethersolvents and, for example, may include dimethylformamide, acetonitrile,dimethyl sulfoxide, or a combination thereof.

As illustrated at 804, the treatment solution and sensor device can beheated while the sensor pad is exposed to treatment solution. In anexample, the treatment solution and the sensor device can be heated at atemperature in a range of 35° C. to 60° C. For example, the temperaturecan be in a range of 40° C. to 50° C.

As illustrated 806, the sensor array can be exposed to the treatmentsolution and optionally heated for a period in a range of 30 seconds to30 minutes. For example, the period can be in a range of 30 seconds to10 minutes, such as a range of 30 seconds to 5 minutes, or even a rangeof 1 minute to 2 minutes.

An organic solvent or water can be used to rinse the sensor array, asillustrated 808, following exposure to the treatment solution. Theorganic solvent can be a low boiling organic solvent. An exemplary lowboiling organic solvent can have a normal boiling point range of 25° C.to 100° C., such as a normal boiling point in a range of 50° C. to 100°C. In an example, the low boiling organic solvent includes an alcohol,such as ethanol or propanol. Alternatively, the organic solvent can beN-methyl pyrrolidone (NMP). Alternatively or in addition, the sensorarray can be rinsed with water, such as deionized water. In a particularexample, the organic solvent is at least partially miscible with waterand the organic solvent of the acid/solvent mixture.

As illustrated at 810, the sensor array can be dried. In an example, thesensor array can be dried under an inert atmosphere, such as using drynitrogen or helium. In another example, the sensor can be heated under adry atmosphere. In a further example, the sensor array can be driedunder vacuum.

In another example illustrated in FIG. 9, a method 900 for treating asensor array includes exposing the sensor array to an organo-siliconsolution followed by applying an acid solution to the sensor array. Forexample, as illustrated at 902, the sensor array is exposed to anorgano-silicon solution that includes an organo-silicon compound and anon-aqueous carrier. In an example, the organo-silicon compound can beselected from the organo-silicon compounds described above. In aparticular example, the organo-silicon compound is a polyalkylsiloxaneor a polyalkyl hydroalkylsiloxane. The non-aqueous carrier can beselected from the organic solvents described above. For example, thenon-aqueous carrier can be an aprotic or non-polar solvent as describedabove. In a particular example, the non-aqueous carrier can be analkane, such as undecane.

As illustrated at 904, an acid solution can be applied to the sensorarray. In an example, the acid solution includes an organic acid, suchas the acids described above. The acid solution can also include anon-aqueous carrier, for example, selected from the organic solventsdescribed above. For example, the non-aqueous carrier can be an aproticor non-polar solvent as described above. In a particular example, thenon-aqueous carrier can be an alkane, such as undecane. Optionally, thenon-aqueous carrier of the organo-silicon solution can be the same asthe non-aqueous carrier of the acid solution. Alternatively, thenon-aqueous carriers are different.

The method 900 can further include heating the sensor in the presence ofthe acid solution, as illustrated at 906, waiting for a period, asillustrated at 908, rinsing, as illustrated at 910, and optionallydrying, as illustrated at 912, in a manner similar to that describedabove in relation to FIG. 8 (804-810). The exposing to theorgano-silicon solution (902) and applying the acid solution (904) canbe repeated prior to drying.

In a further example illustrated in FIG. 10, a method 1000 includesexposing a sensor array to a treatment solution including organo-siliconcompound and an acid, for example, as described above, as illustrated at1002. A sensor device can include the sensor array and optionally a wellstructure defining a well array operatively corresponding to the sensorarray. A well of the well array can expose a sensor pad of a sensor ofthe sensor array. The treatment solution can have the compositiondescribed above. Optionally, the sensor array and the treatment solutioncan be heated, as illustrated at 1004. For example, the sensor array andthe treatment solution can be heated to temperatures described above.

In a further example, the sensor array can be exposed to the treatmentsolution and optionally heated for a period in a range of 30 seconds to30 minutes, as illustrated at 1006. Alternatively, the sensor array canbe exposed to a treatment solution and optionally heated for the timeperiods described above.

Following exposure to the treatment solution, the sensor array can berinsed with a solvent, e.g., a low boiling solvent, as illustrated at1008. Exemplary low boiling solvents are described above. Alternatively,the solvent can be N-methyl pyrrolidone (NMP). The sensor array can berinsed with the low boiling solvent one time or more than one time.

Following rinsing with the low boiling organic solvent, the sensor arraycan be rinsed with water, such as deionized water, as illustrated at1010. Following rinsing with water, the sensor array can be dried, asillustrated at 1012. For example, the sensor array can be exposed to drynitrogen gas.

Once dried, a lid can be applied over the sensor array, as illustratedat 1014. For example, the lid can be attached to the sensor array or anintervening well structure using an adhesive. In particular, the lidincludes fluid ports in fluid communication with a space defined betweenthe lid and a well structure over the sensor array. Optionally, themethod can be applied to a wafer prior to separating the wafer intoarrays and capping individual arrays.

In a further exemplary embodiment illustrated in FIG. 11, a method 1100includes exposing a sensor array to a treatment solution that includesan organo-silicon compound and an acid, as illustrated at 1102. Thetreatment solution can further include an organic solvent. Inparticular, the sensor array can include a well structure defining anarray of wells operatively corresponding to the array of sensors. Asensor pad of a sensor is exposed by a well of the well array. A lid canbe attached over the sensor array or the well array. The lid includesfluid ports in communication with a space defined between the lid andthe well array or sensor array. The treatment solution can be appliedthrough the fluid port into the space. The composition of a treatmentsolution can be as described above.

Optionally, as illustrated at 1104, the treatment solution and thesensor array can be heated. For example, the treatment solution and thesensor array can be heated at the temperatures described above.

The sensor array can be exposed to the treatment solution and optionallyheated for a first period, as illustrated at 1106. The first period canhave a range of 30 seconds to 30 minutes, such as the ranges of timesperiods described above.

In addition, a basic solution can be applied to the sensor array for asecond period, as illustrated at 1108. For example, the basic solutioncan be applied through a fluid port of a lid and into the space definedbetween the lid and the well structure or sensor array. The basicsolution has a pH greater than 7, such as a pH greater than 8, or even apH greater than 9, but generally not greater than 14. The basic solutionincludes a strong base, such as sodium or potassium hydroxide or atetraalkyl ammonium hydroxide, such as tetramethyl ammonium hydroxide ortetraethyl ammonium hydroxide. The base is in a concentration between0.05 M and 1.5 M. For example, the base can be in a concentrationbetween 0.05 M and 1.0 M, such as between 0.05 M and 0.5 M. The sensorarray can be exposed to the basic solution for a period of between 20seconds and 15 minutes, such as a period of between 20 seconds and 5minutes or a period of between 30 seconds and 2 minutes. Alternatively,a weak acid solution can be substituted for the basic solution.

The sensor array can be exposed to the treatment solution followed byexposure to the basic solution or the weak acid repeatedly, such as ktimes. For example, k can be 1, 2, or 3, but generally is not greaterthan 10. Optionally, the organo-silicon compound can be included in thetreatment solution for the first treatment cycle, but not subsequenttreatment cycles. Alternatively, the organo-silicon compound can beincluded in the last treatment cycle, but not prior treatment cycles. Ina further example, the organo-silicon compound can be included in eachof the repeated treatment cycles, or a subset of the treatment cycles.

Following exposure to the treatment solution and the basic solution, thesensor array can be rinsed with the organic solvent or water, asillustrated at 1110. Exemplary low boiling organic solvents includethose described above. Alternatively, the organic solvent can beN-methyl pyrrolidone (NMP). The sensor array can be rinsed with lowboiling organic solvents one or more times, optionally followed by arinse with water between the solvent rinses. Optionally, the sensorarray can be dried, such as with exposure to dry nitrogen, asillustrated at 1112.

The method of FIG. 11 can alternatively be applied to a wafer includingmultiple arrays. The wafer can be separated into individual arrays andlids applied to the individual arrays following drying the wafer.

Such treatment of sensor arrays has been shown to improve loading ofpolymeric beads that incorporating an analyte and secure the analyte inproximity to sensor pads of the sensor array. In particular, suchtreatment improves loading of polymeric beads that includepolynucleotide analytes amplified thereon. For example, such treatmentmethods improve the performance of sequence sequencing devices. Suchtreatment of sensor arrays has been shown to improve sensor signal andsignal-to-noise ratio (SNR), particularly in FET-based sensor arrays.

For example, FIG. 12 illustrates and exemplary sequencing systemenhanced by the above described treatment methods. In a particularexample illustrated in FIG. 12, polymeric particles can be used as asupport for polynucleotides during sequencing techniques. For example,such hydrophilic particles can immobilize a polynucleotide forsequencing using fluorescent sequencing techniques. In another example,the hydrophilic particles can immobilize a plurality of copies of apolynucleotide for sequencing using ion-sensing techniques.Alternatively, the above described treatments can improve polymer matrixbonding to a surface of a sensor array. The polymer matrices can captureanalytes, such as polynucleotides for sequencing.

In general, the polymeric particle can be treated to include abiomolecule, including nucleosides, nucleotides, nucleic acids(oligonucleotides and polynucleotides), polypeptides, saccharides,polysaccharides, lipids, or derivatives or analogs thereof. For example,a polymeric particle can bind or attach to a biomolecule. A terminal endor any internal portion of a biomolecule can bind or attach to apolymeric particle. A polymeric particle can bind or attach to abiomolecule using linking chemistries. A linking chemistry includescovalent or non-covalent bonds, including an ionic bond, hydrogen bond,affinity bond, dipole-dipole bond, van der Waals bond, and hydrophobicbond. A linking chemistry includes affinity between binding partners,for example between: an avidin moiety and a biotin moiety; an antigenicepitope and an antibody or immunologically reactive fragment thereof; anantibody and a hapten; a digoxigen moiety and an anti-digoxigenantibody; a fluorescein moiety and an anti-fluorescein antibody; anoperator and a repressor; a nuclease and a nucleotide; a lectin and apolysaccharide; a steroid and a steroid-binding protein; an activecompound and an active compound receptor; a hormone and a hormonereceptor; an enzyme and a substrate; an immunoglobulin and protein A; oran oligonucleotide or polynucleotide and its corresponding complement.

As illustrated in FIG. 12, a plurality of polymeric particles 1204 canbe placed in a solution along with a plurality of polynucleotides 1202.The plurality of particles 1204 can be activated or otherwise preparedto bind with the polynucleotides 1202. For example, the particles 1204can include an oligonucleotide complementary to a portion of apolynucleotide of the plurality of polynucleotides 1202. In anotherexample, the polymeric particles 1204 can be modified with targetpolynucleotides 1204 using techniques such as biotin-streptavidinbinding.

In a particular embodiment, the hydrophilic particles andpolynucleotides are subjected to polymerase chain reaction (PCR)amplification or recombinase polymerase amplification (RPA). Forexample, dispersed phase droplets 1206 or 1208 are formed as part of anemulsion and can include a hydrophilic particle or a polynucleotide. Inan example, the polynucleotides 1202 and the hydrophilic particles 1204are provided in low concentrations and ratios relative to each othersuch that a single polynucleotide 1202 is likely to reside within thesame dispersed phase droplets as a single hydrophilic particle 1204.Other droplets, such as a droplet 1208, can include a single hydrophilicparticle and no polynucleotide. Each droplet 1206 or 1208 can includeenzymes, nucleotides, salts or other components sufficient to facilitateduplication of the polynucleotide.

In a particular embodiment, an enzyme such as a polymerase is present,bound to, or is in close proximity to the hydrophilic particle orhydrogel particle of the dispersed phase droplet. In an example, apolymerase is present in the dispersed phase droplet to facilitateduplication of the polynucleotide. A variety of nucleic acid polymerasemay be used in the methods described herein. In an exemplary embodiment,the polymerase can include an enzyme, fragment or subunit thereof, whichcan catalyze duplication of the polynucleotide. In another embodiment,the polymerase can be a naturally-occurring polymerase, recombinantpolymerase, mutant polymerase, variant polymerase, fusion or otherwiseengineered polymerase, chemically modified polymerase, syntheticmolecules, or analog, derivative or fragment thereof.

Following PCR or RPA, particles are formed, such as particle 1210, whichcan include the hydrophilic particle 1212 and a plurality of copies 1214of the polynucleotide. While the polynucleotides 1214 are illustrated asbeing on a surface of the particle 1210, the polynucleotides can extendwithin the particle 1210. Hydrogel and hydrophilic particles having alow concentration of polymer relative to water can includepolynucleotide segments on the interior of and throughout the particle1210 or polynucleotides can reside in pores and other openings. Inparticular, the particle 1210 can permit diffusion of enzymes,nucleotides, primers and reaction products used to monitor the reaction.A high number of polynucleotides per particle can produce a bettersignal.

In embodiments, polymeric particles from an emulsion-breaking procedurecan be collected and washed in preparation for sequencing. Collectioncan be conducted by contacting biotin moieties (e.g., linked toamplified polynucleotide templates which are attached to the polymericparticles) with avidin moieties, and separation away from polymericparticles lacking biotinylated templates. Collected polymeric particlesthat carry double-stranded template polynucleotides can be denatured toyield single-stranded template polynucleotides for sequencing.Denaturation steps can include treatment with base (e.g., NaOH),formamide, or pyrrolidone.

In an exemplary embodiment, the particle 1210 can be utilized in asequencing device. For example, a sequencing device 1216 can include anarray of wells 1218. The sequencing device 1216 can be treated with atreatment solution including sulfonic acid, as described above. Aparticle 1210 can be placed within a well 1218.

In an example, a primer can be added to the wells 1218 or the particle1210 can be pre-exposed to the primer prior to placement in the well1218. In particular, the particle 1210 can include bound primer. Theprimer and polynucleotide form a nucleic acid duplex including thepolynucleotide (e.g., a template nucleic acid) hybridized to the primer.The nucleic acid duplex is an at least partially double-strandedpolynucleotide. Enzymes and nucleotides can be provided to the well 1218to facilitate detectible reactions, such as nucleotide incorporation.

Sequencing can be performed by detecting nucleotide addition. Nucleotideaddition can be detected using methods such as fluorescent emissionmethods or ion detection methods. For example, a set of fluorescentlylabeled nucleotides can be provided to the system 1216 and can migrateto the well 1218. Excitation energy can be also provided to the well1218. When a nucleotide is captured by a polymerase and added to the endof an extending primer, a label of the nucleotide can fluoresce,indicating which type of nucleotide is added.

In an alternative example, solutions including a single type ofnucleotide can be fed sequentially. In response to nucleotide addition,the pH within the local environment of the well 1218 can change. Such achange in pH can be detected by ion sensitive field effect transistors(ISFET). As such, a change in pH can be used to generate a signalindicating the order of nucleotides complementary to the polynucleotideof the particle 1210.

In particular, a sequencing system can include a well, or a plurality ofwells, disposed over a sensor pad of an ionic sensor, such as a fieldeffect transistor (FET). In embodiments, a system includes one or morepolymeric particles loaded into a well which is disposed over a sensorpad of an ionic sensor (e.g., FET), or one or more polymeric particlesloaded into a plurality of wells which are disposed over sensor pads ofionic sensors (e.g., FET). In embodiments, a FET can be a chemFET or anISFET. A “chemFET” or chemical field-effect transistor, includes a typeof field effect transistor that acts as a chemical sensor. The chemFEThas the structural analog of a MOSFET transistor, where the charge onthe gate electrode is applied by a chemical process. An “ISFET” orion-sensitive field-effect transistor, can be used for measuring ionconcentrations in solution; when the ion concentration (such as H+)changes, the current through the transistor changes accordingly.

In embodiments, the FET may be a FET array. As used herein, an “array”is a planar arrangement of elements such as sensors or wells. The arraymay be one or two dimensional. A one dimensional array can be an arrayhaving one column (or row) of elements in the first dimension and aplurality of columns (or rows) in the second dimension. The number ofcolumns (or rows) in the first and second dimensions may or may not bethe same. The FET array can comprise 10², 10³, 10⁴, 10⁵, 10⁶, 10⁷ ormore FETs, but generally not more than 10¹².

In embodiments, one or more microfluidic structures can be fabricatedabove the FET sensor array to provide for containment or confinement ofa biological or chemical reaction. For example, in one implementation,the microfluidic structure(s) can be configured as one or more wells (ormicrowells, or reaction chambers, or reaction wells, as the terms areused interchangeably herein) disposed above one or more sensors of thearray, such that the one or more sensors over which a given well isdisposed detect and measure analyte presence, level, or concentration inthe given well. In embodiments, there can be a 1:1 correspondence of FETsensors and reaction wells.

Returning to FIG. 12, in another example, a well 1218 of the array ofwells can be operatively connected to measuring devices. For example,for fluorescent emission methods, a well 1218 can be operatively coupledto a light detection device. In the case of ionic detection, the lowersurface of the well 1218 may be disposed over a sensor pad of an ionicsensor, such as a field effect transistor.

One exemplary system involving sequencing via detection of ionicbyproducts of nucleotide incorporation is the Ion Torrent™ PGM™,Proton™, or S5™ sequencer (Thermo Fisher Scientific), which is anion-based sequencing system that sequences nucleic acid templates bydetecting hydrogen ions produced as a byproduct of nucleotideincorporation. Typically, hydrogen ions are released as byproducts ofnucleotide incorporations occurring during template-dependent nucleicacid synthesis by a polymerase. The Ion Torrent™ PGM™, Proton™, or S5™sequencer detects the nucleotide incorporations by detecting thehydrogen ion byproducts of the nucleotide incorporations. The IonTorrent™ PGM™, Proton™, or S5™ sequencer can include a plurality oftemplate polynucleotides to be sequenced, each template disposed withina respective sequencing reaction well in an array. The wells of thearray can each be coupled to at least one ion sensor that can detect therelease of H+ ions or changes in solution pH produced as a byproduct ofnucleotide incorporation. The ion sensor comprises a field effecttransistor (FET) coupled to an ion-sensitive detection layer that cansense the presence of H+ ions or changes in solution pH. The ion sensorcan provide output signals indicative of nucleotide incorporation whichcan be represented as voltage changes whose magnitude correlates withthe H+ ion concentration in a respective well or reaction chamber.Different nucleotide types can be flowed serially into the reactionchamber, and can be incorporated by the polymerase into an extendingprimer (or polymerization site) in an order determined by the sequenceof the template. Each nucleotide incorporation can be accompanied by therelease of H+ ions in the reaction well, along with a concomitant changein the localized pH. The release of H+ ions can be registered by the FETof the sensor, which produces signals indicating the occurrence of thenucleotide incorporation. Nucleotides that are not incorporated during aparticular nucleotide flow may not produce signals. The amplitude of thesignals from the FET can also be correlated with the number ofnucleotides of a particular type incorporated into the extending nucleicacid molecule thereby permitting homopolymer regions to be resolved.Thus, during a run of the sequencer multiple nucleotide flows into thereaction chamber along with incorporation monitoring across amultiplicity of wells or reaction chambers can permit the instrument toresolve the sequence of many nucleic acid templates simultaneously.

Embodiments of the above described treatment methods and sensorapparatuses treated using such methods exhibit technical advantagesincluding improved nucleic acid particle loading or signal quality.Improvements in particle loading or signal strength further enhanceanalysis techniques, such as base-calling and sequencing. It is believedthat some technical advantages are derived from activation oforgano-silicon compounds, for example, through acid catalyzed breakingof siloxane bonds, which then react with hydroxyl groups associated withthe surfaces of metal or semi-metal oxides.

EXAMPLES Example 1

Organo-silicon compounds are tested for influence on buffering,signal-to-noise, key signal, and Q20 mean using an ION Torrent® Proton Ion an ION Torrent® Proton Sequencer. A solution of undecane including 5wt % dodecyl benzene sulfonic acid and 5 wt % of the selectedorgano-silicon compound are applied through ports of a Proton I chip andremain in contact with sensor surfaces for approximately 2 minutes. TheProton I chips are flushed with water and isopropyl alcohol. A 5 wt %DBSA in undecane solution is applied through port of the Proton I chipfollowed by a base solution including 10 mM NaOH. The DBSA and NaOHtreatment is repeated three times. The Proton I chip is then flushedwith water and isopropyl alcohol.

The Proton I chip is loaded with nucleic acid beads using an ION Chef™under standard protocols. The Proton I chip is applied to the ProtonSequencer and standard testing is performed to determine buffering,loading, signal-to-noise, key signal, and q20 mean measurements.

The organo-silicon compound is selected from hydride-terminatedpolydimethylsiloxane, 2,2,4,4,6,6-hexamethylcyclotrisilazane, monovinylfunctional polydimethylsiloxane (PDMS), platinum-cyclovinylmethylsiloxane, phenyldimethylchlorosilane, triisopropylsiyltrifluoromethanesulfonate, tert-butylchlorodiiphenylsilane, monohydrideterminated PDMS, chlorotripropylsilane, (N,N-dimethylamino)trimethyl-silane, tris(trimethylsilyl)silane, triethylchlorosilane,3-cyanopropyldimethylchloro-silane, chlorotriethylsilane,hydride-terminated polydimethylsiloxane (PDMS),1,3-dichloro-1,1,3,3-tetramethyldisiloxane,1,2-bis(chlorodimethylsiyl)ethane, trimethylsilyltrifluoronesulfonate,trioctylsilane, dodecyldimethylchlorosilane, chlorodimethylthexylsilane,trimethylchlorosilane, hexamethyltrisiloxane, chloro(chloromethyl)dimethylsilane, polymethylhydrosiloxane, thexyldimethylchlorosilane,vinyl terminated PDMS, triisopropylchlorosilane, vinyl terminated PDMS,trimethylmethoxysilane, tris(trimethylsilyloxy)silane,octamethyltrisiloxane, trimethylchlorosilane, chlorotriisopropylsilane,or acetoxytrimethylsilane. Some species of PDMS are also tested incombination with a platinum catalyst, platinum-cyclovinylmethylsiloxane.

As illustrated in FIG. 13, many of the organo-silicon compounds provideddesirably low buffering following the three treatments with DBSA andNaOH. Some species provide buffering of less than 100, particularly lessthan 90, with some species providing buffering in a range of 50 to 80.In particular, higher molecular weight PDMS species provided lowbuffering and offer additional advantages in easy of handling.

FIG. 14 illustrates signal-to-noise ratios for a subset of specieshaving buffering of less than 100. Several of the high molecular weightPDMS species provide desirable signal-to-noise greater than 12, withsome providing a signal-to-noise of greater than 12.3. Such highmolecular weight PDMS species also provide desirable key signal ofgreater than 90, as illustrated in FIG. 15. Other species oforgano-silicon compounds also provide desirable key signal.

When utilized on a sequencing platform, the organo-silicon compoundsprovide for improved sequencing as indicated by q20 mean and illustratedin FIG. 16. In particular, several higher molecular weight PDMS speciesprovide significantly improved q20 mean.

Example 2

Organo-silicon compounds selected from non-functionalized PDMS havingmolecular weight of 750 Da, 900 Da, 1200 Da, 2000 Da, 3700 Da, or 6000Da are tested for influence on buffering, signal-to-noise, key signal,and q20 mean using an ION Torrent® Proton I on an ION Torrent® ProtonSequencer. A solution of undecane including 5 wt % dodecyl benzenesulfonic acid and 5 wt % of the selected organo-silicon compound areapplied through ports of a Proton I chip and remain in contact withsensor surfaces for approximately 2 minutes. The Proton I chip isflushed with water and isopropyl alcohol. A 5 wt % DBSA in undecanesolution is applied through port of the Proton I chip followed by a basesolution including 10 mM NaOH. The DBSA and NaOH treatment is repeatedthree times. The Proton I chip is then flushed with water and isopropylalcohol. A control is formed using three DBSA and NaOH treatmentswithout exposure to an organo-silicon compound.

The Proton I chip is loaded with nucleic acid beads using an ION Chefunder standard protocols. The Proton I chip is applied to the ProtonSequencer and standard testing is performed to determine buffering,loading, signal-to-noise, key signal, and q20 mean measurements.

TABLE Effect of PDMS on Performance MW Loading PDMS Buffering (%)q20mean Control 88 750 71 90.0 163.0 900 69 89.7 165.0 1200 68 90.6169.0 2000 67 90.2 171.0 3700 70 6000 64

Each of the PDMS treated Proton I chips exhibit improved buffering andq20mean relative to the control chip. In addition, lower buffering andimproved q20mean generally follows increased PDMS molecular weight.

Example 3

A solution of undecane including 5 wt % PDMS is applied through ports ofa Proton I chip and remains in contact with sensor surfaces forapproximately 1 minute. A second solution including undecane and 5 wt %DBSA is applied through ports of a Proton I chip, flushing at least aportion of the first solution from the chip, and remains in contact withsensor surfaces for approximately 2 minute. The Proton I chip is flushedwith water and isopropyl alcohol. A base solution including 10 mM NaOHis applied for 60 seconds. The DBSA and NaOH treatment is repeated threetimes. The Proton I chip is then flushed with water and isopropylalcohol.

The Proton I chip is loaded with nucleic acid beads using an ION Chefunder standard protocols. The Proton I chip is applied to the ProtonSequencer and standard testing is performed to determine buffering,loading, signal-to-noise, key signal, and q20 mean measurements.

In a first aspect, a method of treating a sensor array including aplurality of sensors and an isolation structure, where a sensor of theplurality of sensors has a sensor pad exposed at a surface of the sensorarray and the isolation structure is disposed between the sensor pad andsensor pads of other sensors of the plurality of sensors, comprisesexposing the sensor pad and the isolation structure to a non-aqueousorgano-silicon solution including an organo-silicon compound and a firstnon-aqueous carrier; applying an acid solution including an organic acidand a second non-aqueous carrier to the sensor pad; and rinsing the acidsolution from the sensor pad and the isolation structure.

In an example of the first aspect, a portion of the organo-siliconcompound remains on the isolation structure.

In another example of the first aspect and the above example, theorgano-silicon compound includes a silane functionalized with an aryl,polyaryl, alkyl, alkoxy, halo, or cyano moiety, or any combinationthereof. For example, the silane is selected from the group consistingof phenyldimethylchlorosilane, tert-butylchlorodiiphenylsilane,chlorotripropylsilane, (N,N-dimethylamino) trimethyl-silane,tris(trimethylsilyl)silane, triethylchlorosilane,3-cyanopropyldimethylchloro-silane, chlorotriethylsilane,1,2-bis(chlorodimethylsiyl)ethane, trimethylsilyltrifluoronesulfonate,trioctylsilane, dodecyldimethylchlorosilane, chlorodimethylthexylsilane,trimethylchlorosilane, chloro(chloromethyl) dimethylsilane,thexyldimethylchlorosilane, triisopropylchlorosilane,trimethylmethoxysilane, trimethylchlorosilane, chlorotriisopropylsilane,acetoxytrimethylsilane, and a combination thereof.

In a further example of the first aspect and the above example, theorgano-silicon compound includes a polysiloxane including aryl, dialkylor alkylhydro units, or combinations thereof. For example, the aryl unitincludes a phenylalkyl siloxyl unit. In an example, the dilkyl unit orthe alkylhydro unit includes an alkyl moiety selected from methyl,ethyl, propyl, butyl moieties, and a combination thereof. In a furtherexample, the organo-silicon compound include a siloxane selected fromthe group consisting of an alkyl terminated polydimethylsiloxane, ahydride-terminated polydimethylsiloxane, a monovinyl terminatedpolydimethylsiloxane, dichloro-tetramethyldisiloxane,hexamethyltrisiloxane, polymethylhydrosiloxane,tris(trimethylsilyloxy)silane, octamethyltrisiloxane, and a combinationthereof.

In an additional example of the first aspect and the above example, theorgano-silicon compound includes a silazane.

In another example of the first aspect and the above example, theorgano-silicon compound has a molecular weight in a range of 50 Da to10000 Da. For example, the molecular weight is in a range of 100 Da to8000 Da. In a further example, the molecular weight is in a range of 500Da to 7000 Da.

In a further example of the first aspect and the above example, theorgano-silicon solution includes the organo-silicon compound in anamount of 0.001% to 10.0% by weight. For example, the amount is in arange of 0.005% to 5.0% by weight.

In an additional example of the first aspect and the above example, theorgano-silicon solution further includes a platinum compound.

In another example of the first aspect and the above example, theorganic acid includes sulfonic acid. For example, the sulfonic acidincludes alkyl sulfonic acid, alkyl aryl sulfonic acid, or a combinationthereof. In an example, the alkyl aryl sulfonic acid includes an alkylgroup having between 1 and 20 carbons. In another example, the sulfonicacid includes dodecyl benzene sulfonic acid.

In a further example of the first aspect and the above example, thetreatment solution includes between 0.5 wt % and 25 wt % of the organicacid.

In an additional example of the first aspect and the above example, thefirst or second non-aqueous carrier is non-polar.

In another example of the first aspect and the above example, the firstor second non-aqueous carrier has a normal boiling point in a range of36° C. to 345° C.

In a further example of the first aspect and the above example, thefirst or second non-aqueous carrier is an alkane having between 6 and 24carbons.

In an additional example of the first aspect and the above example, themethod further includes heating the sensor pad, the isolation structure,and the treatment solution while exposing the sensor pad to thetreatment solution. For example, heating includes heating at atemperature in a range of 35° C. to 70° C.

In another example of the first aspect and the above example, exposingincludes exposing for a period in a range of 30 seconds to 30 minutes.

In a further example of the first aspect and the above example, themethod further includes exposing at least the sensor pad to a basicsolution. For example, the basic solution includes between 0.005M and1.5M sodium hydroxide. In another example, exposing at least the sensorpad to the basic solution occurs following exposing the sensor pad tothe treatment solution. In a further example, the method furtherincludes repeating exposing at least the sensor pad to the acid solutionand exposing at least the sensor pad to the basic solution.

In an additional example of the first aspect and the above example,rinsing includes rinsing with a rinse organic solvent miscible withwater and the first or second non-aqueous carrier.

In another example of the first aspect and the above example, rinsingincludes rinsing with a low boiling organic solvent having a normalboiling point in a range of 25° C. to 100° C. In an example, the lowboiling organic solvent includes alcohol.

In a further example of the first aspect and the above example, rinsingincludes rinsing with water.

In a second aspect, a method of treating a sensor array including aplurality of sensors and an isolation structure, wherein a sensor of theplurality of sensors has a sensor pad exposed at a surface of the sensorarray and the isolation structure is disposed between the sensor pad andsensor pads of other sensors of the plurality of sensors, comprisesexposing at least the sensor pad and the isolation structure to atreatment solution including an organo-silicon compound, an organicacid, and an organic solvent; and rinsing the treatment solution fromthe sensor pad.

In an example of the second aspect, the organo-silicon compound includesa silane functionalized with an aryl, polyaryl, alkyl, alkoxy, halo, orcyano moiety, or any combination thereof. For example, the silane isselected from the group consisting of phenyldimethylchlorosilane,tert-butylchlorodiiphenylsilane, chlorotripropylsilane,(N,N-dimethylamino) trimethyl-silane, tris(trimethylsilyl)silane,triethylchlorosilane, 3-cyanopropyldimethylchloro-silane,chlorotriethylsilane, 1,2-bis(chlorodimethylsiyl)ethane,trimethylsilyltrifluoronesulfonate, trioctylsilane,dodecyldimethylchlorosilane, chlorodimethylthexylsilane,trimethylchlorosilane, chloro(chloromethyl) dimethylsilane,thexyldimethylchlorosilane, triisopropylchlorosilane,trimethylmethoxysilane, trimethylchlorosilane, chlorotriisopropylsilane,acetoxytrimethylsilane, and a combination thereof.

In another example of the second aspect and the above example, theorgano-silicon compound includes a polysiloxane including aryl, dialkylor alkylhydro units, or combinations thereof. For example, the aryl unitincludes a phenylalkyl siloxyl unit. In an example, the dilkyl unit orthe alkylhydro unit includes an alkyl moiety selected from methyl,ethyl, propyl, butyl moieties, and a combination thereof. In anotherexample, the organo-silicon compound include a siloxane selected fromthe group consisting of an alkyl terminated polydimethylsiloxane, ahydride-terminated polydimethylsiloxane, a monovinyl terminatedpolydimethylsiloxane, dichloro-tetramethyldisiloxane,hexamethyltrisiloxane, polymethylhydrosiloxane,tris(trimethylsilyloxy)silane, octamethyltrisiloxane, and a combinationthereof.

In a further example of the second aspect and the above example, theorgano-silicon compound includes a silazane.

In an additional example of the second aspect and the above example, theorgano-silicon compound has a molecular weight in a range of 50 Da to10000 Da. In an example, the molecular weight is in a range of 100 Da to8000 Da. For example, the molecular weight is in a range of 500 Da to7000 Da.

In another example of the second aspect and the above example, thetreatment solution includes the organo-silicon compound in an amount of0.001% to 10.0% by weight. For example, the amount is in a range of0.005% to 5.0% by weight.

In a further example of the second aspect and the above example, thetreatment solution further includes a platinum compound.

In an additional example of the second aspect and the above example, theacid includes sulfonic acid. In an example, the sulfonic acid includesalkyl sulfonic acid, alkyl aryl sulfonic acid, or a combination thereof.For example, the alkyl aryl sulfonic acid includes an alkyl group havingbetween 1 and 20 carbons.

In another example of the second aspect and the above example, thesulfonic acid includes dodecyl benzene sulfonic acid.

In a further example of the second aspect and the above example, thetreatment solution includes between 0.5 wt % and 25 wt % of the acid.

In an additional example of the second aspect and the above example, theorganic solvent is non-polar.

In another example of the second aspect and the above example, theorganic solvent has a normal boiling point in a range of 36° C. to 345°C.

In a further example of the second aspect and the above example, theorganic solvent is an alkane having between 6 and 24 carbons.

In an additional example of the second aspect and the above example, themethod further includes heating the sensor pad and the treatmentsolution while exposing the sensor pad to the treatment solution. Forexample, heating includes heating at a temperature in a range of 35° C.to 70° C.

In another example of the second aspect and the above example, exposingincludes exposing for a period in a range of 30 seconds to 30 minutes.

In a further example of the second aspect and the above example, themethod further includes exposing at least the sensor pad to a basicsolution. In an example, the basic solution includes between 0.005M and1.5M sodium hydroxide. For example, exposing at least the sensor pad tothe basic solution occurs following exposing the sensor pad to thetreatment solution. In an another example, the method further includesrepeating exposing at least the sensor pad to the treatment solution andexposing at least the sensor pad to the basic solution.

In an additional example of the second aspect and the above example,rinsing includes rinsing with a rinse organic solvent miscible withwater and the organic solvent.

In another example of the second aspect and the above example, rinsingincludes rinsing with a low boiling organic solvent having a normalboiling point in a range of 25° C. to 100° C. For example, the lowboiling organic solvent includes alcohol.

In a further example of the second aspect and the above example, rinsingincludes rinsing with water.

In a third aspect, a method of treating a sensor array including aplurality of sensors, wherein a sensor of the plurality of the sensorsincludes a sensor pad, a well structure defines a well arraycorresponding with the sensor array, a well of the well array exposesthe sensor pad, a lid is attached over the sensor array and the wellstructure and including an fluid port, and a space is defined betweenthe lid and the well structure, comprises applying a treatment solutionthrough the fluid port into the space and waiting for a first periodbetween 30 seconds and 30 minutes, the treatment solution including anorgano-silicon compound, an acid and an organic solvent; applying abasic solution through the fluid port into the space and waiting for asecond period between 20 seconds and 15 minutes; and applying a rinsesolution through the fluid port.

In an example of the third aspect, the method further includes repeatingapplying the treatment solution, applying the basic solution, andapplying the rinse solution.

In a fourth aspect, a method of treating a sensor array including aplurality of sensors, wherein a sensor of the plurality of the sensorsincludes a sensor pad, a well structure defines a well arraycorresponding with the sensor array, and a well of the well arrayexposes the sensor pad, comprises applying a treatment solution to atleast the sensor pad and waiting for a first period between 30 secondsand 30 minutes, the treatment solution including an organo-siliconcompound, an acid and an organic solvent; rinsing at least the sensorpad with a low boiling organic solvent; and drying the sensor array.

In an example of the fourth aspect, the method further includes rinsingwith water following rinsing with the low boiling organic solvent andprior to drying.

In another example of the fourth aspect and the above example, themethod further includes attaching a lid over the sensor array and thewell array, the lid including a fluid port, a space defined between thelid and the well array in fluid communication with the fluid port.

In a fifth aspect, a sensor device is treated by the method of any oneof the above aspects and examples.

In a sixth aspect, a solution includes 0.001 wt % to 10.0 wt % of anorgano-silicon compound, 2.5 wt % to 5 wt % dodecyl benzene sulfonicacid and a non-polar linear alkane having between 6 and 18 carbons.

In a seventh aspect, a kit includes a nucleotide solution including atleast one nucleotide type; polymeric particles; and a treatment solutionincluding 0.001 wt % to 10.0 wt % of an organo-silicon compound, 0.5 wt% to 20 wt % sulfonic acid and an organic solvent having a normalboiling point in a range of 65° C. to 275° C.

In a further example of the above aspects and examples, theorgano-silicon compound includes a polysiloxane including hydrophilic,polar, or amphiphilic units, or combinations thereof.

Note that not all of the activities described above in the generaldescription or the examples are required, that a portion of a specificactivity may not be required, and that one or more further activitiesmay be performed in addition to those described. Still further, theorder in which activities are listed are not necessarily the order inwhich they are performed.

Particular salts of above described acids or bases can have activity,and may be useful in the above described methods. Salts include alkalior alkali earth metal salts, or tetraalkylammonium salts of the aboveacids or bases.

In the foregoing specification, the concepts have been described withreference to specific embodiments. However, one of ordinary skill in theart appreciates that various modifications and changes can be madewithout departing from the scope of the invention as set forth in theclaims below. Accordingly, the specification and figures are to beregarded in an illustrative rather than a restrictive sense, and allsuch modifications are intended to be included within the scope ofinvention.

As used herein, the terms “comprises,” “comprising,” “includes,”“including,” “has,” “having” or any other variation thereof, areintended to cover a non-exclusive inclusion. For example, a process,method, article, or apparatus that comprises a list of features is notnecessarily limited only to those features but may include otherfeatures not expressly listed or inherent to such process, method,article, or apparatus. Further, unless expressly stated to the contrary,“or” refers to an inclusive-or and not to an exclusive-or. For example,a condition A or B is satisfied by any one of the following: A is true(or present) and B is false (or not present), A is false (or notpresent) and B is true (or present), and both A and B are true (orpresent).

Also, the use of “a” or “an” are employed to describe elements andcomponents described herein. This is done merely for convenience and togive a general sense of the scope of the invention. This descriptionshould be read to include one or at least one and the singular alsoincludes the plural unless it is obvious that it is meant otherwise.

Benefits, other advantages, and solutions to problems have beendescribed above with regard to specific embodiments. However, thebenefits, advantages, solutions to problems, and any feature(s) that maycause any benefit, advantage, or solution to occur or become morepronounced are not to be construed as a critical, required, or essentialfeature of any or all the claims.

After reading the specification, skilled artisans will appreciate thatcertain features are, for clarity, described herein in the context ofseparate embodiments, may also be provided in combination in a singleembodiment. Conversely, various features that are, for brevity,described in the context of a single embodiment, may also be providedseparately or in any subcombination. Further, references to valuesstated in ranges include each and every value within that range.

What is claimed is:
 1. A method of treating a sensor array, the sensorarray including a plurality of sensors, a sensor of the plurality of thesensors including a sensor pad, a well structure defining a well arraycorresponding with the sensor array, a well of the well array exposingthe sensor pad, the method comprising: applying a treatment solution toat least the sensor pad and waiting for a first period between 30seconds and 30 minutes, the treatment solution including anorgano-silicon compound, an acid and an organic solvent; rinsing atleast the sensor pad with a low boiling organic solvent; and drying thesensor array.
 2. The method of claim 1, further comprising rinsing withwater following rinsing with the low boiling organic solvent and priorto drying.
 3. The method of claim 1, further comprising attaching a lidover the sensor array and the well array, the lid including a fluidport, a space defined between the lid and the well array in fluidcommunication with the fluid port.
 4. The method of claim 1, wherein theorgano-silicon compound includes a silane functionalized with an aryl,polyaryl, alkyl, alkoxy, halo, or cyano moiety, or any combinationthereof.
 5. The method of claim 4, wherein the silane is selected fromthe group consisting of phenyldimethylchlorosilane,tert-butylchlorodiiphenylsilane, chlorotripropylsilane,(N,N-dimethylamino) trimethyl-silane, tris(trimethylsilyl)silane,triethylchlorosilane, 3-cyanopropyldimethylchloro-silane,chlorotriethylsilane, 1,2-bis(chlorodimethylsiyl)ethane,trimethylsilyltrifluoronesulfonate, trioctylsilane,dodecyldimethylchlorosilane, chlorodimethylthexylsilane,trimethylchlorosilane, chloro(chloromethyl) dimethylsilane,thexyldimethylchlorosilane, triisopropylchlorosilane,trimethylmethoxysilane, trimethylchlorosilane, chlorotriisopropylsilane,acetoxytrimethylsilane, and a combination thereof.
 6. The method ofclaim 1, wherein the organo-silicon compound includes a polysiloxaneincluding aryl, dialkyl or alkylhydro units, or combinations thereof. 7.The method of claim 6, wherein the organo-silicon compound includes asiloxane selected from the group consisting of an alkyl terminatedpolydimethylsiloxane, a hydride-terminated polydimethylsiloxane, amonovinyl terminated polydimethylsiloxane,dichloro-tetramethyldisiloxane, hexamethyltrisiloxane,polymethylhydrosiloxane, tris(trimethylsilyloxy)silane,octamethyltrisiloxane, and a combination thereof.
 8. The method of claim1, wherein the organo-silicon compound has a molecular weight in a rangeof 50 Da to 10000 Da.
 9. The method of claim 1, wherein the treatmentsolution includes the organo-silicon compound in an amount of 0.001% to10.0% by weight.
 10. The method of claim 1, wherein the treatmentsolution further includes a platinum compound.
 11. The method of claim1, wherein the organic acid includes sulfonic acid.
 12. The method ofclaim 11, wherein the sulfonic acid includes alkyl sulfonic acid, alkylaryl sulfonic acid, or a combination thereof.
 13. The method of claim12, wherein the alkyl aryl sulfonic acid includes an alkyl group havingbetween 1 and 20 carbons.
 14. The method of claim 1, wherein thetreatment solution includes between 0.5 wt % and 25 wt % of the acid.15. The method of claim 1, wherein the organic solvent is non-polar. 16.The method of claim 1, wherein the organic solvent has a normal boilingpoint in a range of 36° C. to 345° C.
 17. The method of claim 1, furthercomprising heating the sensor pad and the treatment solution whileexposing the sensor pad to the treatment solution, wherein heatingincludes heating at a temperature in a range of 35° C. to 70° C.
 18. Themethod of claim 1, further comprising exposing at least the sensor padto a basic solution.
 19. The method of claim 1, wherein rinsing includesrinsing with a low boiling organic solvent having a normal boiling pointin a range of 25° C. to 100° C.
 20. The method of claim 19, wherein thelow boiling organic solvent includes alcohol.